LAMMPS (19 Nov 2024 - Development - patch_5May2020-20901-g8641486249-modified)
# Example problem demonstrating the use of synchronized_verlet
# Refer https://doi.org/10.1016/j.cpc.2025.109524 for further details

units	        si
atom_style	sphere
newton off

boundary   	p p f
read_data       3ps.dat
Reading data file ...
  orthogonal box = (-0.03 -0.02 -0.02) to (0.03 0.02 0.02)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  3 atoms
  reading velocities ...
  3 velocities
  read_data CPU = 0.003 seconds

group           ps type 1
2 atoms in group ps
group           fine type 2
1 atoms in group fine

pair_style granular
pair_coeff * * hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution synchronized_verlet
# pair_coeff * * hertz/material 5e8 0.5 0.3 tangential mindlin  NULL 0.0 0.5 damping coeff_restitution #synchronized_verlet

timestep        1e-6
fix             frz ps freeze
fix             g fine gravity 9.81 vector 0 0 -1
fix             1 fine nve/sphere
fix             2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane $(zlo) $(zhi)
fix             2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane -0.020000000000000000416 $(zhi)
fix             2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane -0.020000000000000000416 0.020000000000000000416

dump            1 all custom 3000 op.dump id x y z vx vy vz type diameter

comm_modify     vel yes

thermo          3000
thermo_style    custom step ke
run_style       verlet
run             300000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 0.011
  ghost atom cutoff = 0.011
  binsize = 0.0055, bins = 11 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair granular, perpetual
      attributes: half, newton off, size, history
      pair build: half/size/bin/atomonly/newtoff
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.34 | 10.34 | 10.34 Mbytes
   Step         KinEng    
         0   0            
      3000   7.7090573e-16
      6000   3.11122e-15  
      9000   7.1189829e-15
     12000   1.2962539e-14
     15000   2.0887458e-14
     18000   3.1226589e-14
     21000   4.4413694e-14
     24000   6.1001238e-14
     27000   8.1683111e-14
     30000   1.0732325e-13
     33000   1.3899142e-13
     36000   1.7800759e-13
     39000   2.2599689e-13
     42000   2.849574e-13 
     45000   3.5734355e-13
     48000   4.4616861e-13
     51000   5.5513052e-13
     54000   6.8876606e-13
     57000   8.5263971e-13
     60000   1.0535747e-12
     63000   1.2999356e-12
     66000   1.6019734e-12
     69000   1.9722472e-12
     72000   2.4261384e-12
     75000   2.9824767e-12
     78000   3.6643038e-12
     81000   4.4997992e-12
     84000   5.5234053e-12
     87000   6.7771879e-12
     90000   8.3124767e-12
     93000   1.0191838e-11
     96000   1.2491433e-11
     99000   1.5303816e-11
    102000   1.8741238e-11
    105000   2.2939491e-11
    108000   2.8062329e-11
    111000   3.4306457e-11
    114000   4.1907005e-11
    117000   5.114332e-11 
    120000   6.2344723e-11
    123000   7.5895667e-11
    126000   9.2239362e-11
    129000   1.118785e-10 
    132000   1.3537107e-10
    135000   1.6331855e-10
    138000   1.96343e-10  
    141000   2.3504868e-10
    144000   2.799638e-10 
    147000   4.4767299e-10
    150000   8.5696526e-10
    153000   1.4079769e-09
    156000   2.1007079e-09
    159000   2.9351582e-09
    162000   3.9113279e-09
    165000   5.029217e-09 
    168000   6.2888254e-09
    171000   7.6901531e-09
    174000   9.2332002e-09
    177000   1.0917967e-08
    180000   1.2744453e-08
    183000   1.4712658e-08
    186000   1.6822582e-08
    189000   1.9074226e-08
    192000   2.1467589e-08
    195000   2.4002672e-08
    198000   2.6679474e-08
    201000   2.9497995e-08
    204000   3.2458236e-08
    207000   6.543991e-09 
    210000   5.3049419e-09
    213000   4.2076122e-09
    216000   3.2520018e-09
    219000   2.4381108e-09
    222000   1.7659392e-09
    225000   1.2354868e-09
    228000   8.4675389e-10
    231000   5.997403e-10 
    234000   4.9444606e-10
    237000   5.3087117e-10
    240000   7.0901564e-10
    243000   1.0288795e-09
    246000   1.4904626e-09
    249000   2.0937652e-09
    252000   2.8387871e-09
    255000   3.7255283e-09
    258000   4.7539889e-09
    261000   5.9241689e-09
    264000   7.2360682e-09
    267000   1.6704365e-09
    270000   1.161387e-09 
    273000   7.9405678e-10
    276000   5.6844595e-10
    279000   4.8455448e-10
    282000   5.4238236e-10
    285000   7.419296e-10 
    288000   1.0831962e-09
    291000   1.5661821e-09
    294000   8.41555e-10  
    297000   5.7599278e-10
    300000   4.5214992e-10
Loop time of 0.193539 on 1 procs for 300000 steps with 3 atoms

98.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.064036   | 0.064036   | 0.064036   |   0.0 | 33.09
Neigh   | 0.00015725 | 0.00015725 | 0.00015725 |   0.0 |  0.08
Comm    | 0.027944   | 0.027944   | 0.027944   |   0.0 | 14.44
Output  | 0.002992   | 0.002992   | 0.002992   |   0.0 |  1.55
Modify  | 0.059704   | 0.059704   | 0.059704   |   0.0 | 30.85
Other   |            | 0.03871    |            |       | 20.00

Nlocal:              3 ave           3 max           3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              1 ave           1 max           1 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              1 ave           1 max           1 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1
Ave neighs/atom = 0.33333333
Neighbor list builds = 70
Dangerous builds = 0
Total wall time: 0:00:00
